6HDO | pdb_00006hdo

Crystal structure of human ATAD2 bromodomain in complex with 8-(((1R,2R,3R,5S)-2-(2-(1,1-dioxidotetrahydro-2H-thiopyran-4-yl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)quinolin-2(1H)-one


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2770.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate and 20-25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.9668.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.254α = 90
b = 79.254β = 90
c = 135.033γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002013-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.61135.0399.620.810.38153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.612.7510010.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.6137.64773537499.820.186460.184270.190.231940.23RANDOM48.947
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.280.140.28-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.451
r_dihedral_angle_4_deg21.687
r_dihedral_angle_3_deg16.005
r_long_range_B_refined12.261
r_long_range_B_other12.102
r_scangle_other11.181
r_mcangle_it8.049
r_mcangle_other8.043
r_scbond_it7.831
r_scbond_other7.741
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1077
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling